BALL: reconstructFragmentProcessor.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 
00005 #ifndef BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H
00006 #define BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H
00007 
00008 #include <list>
00009 
00010 #ifndef BALL_COMMON_H
00011 # include <BALL/common.h>
00012 #endif
00013 
00014 #ifndef BALL_DATATYPE_TRIPLE_H
00015 # include <BALL/DATATYPE/triple.h>
00016 #endif
00017 
00018 #ifndef BALL_MATHS_MATRIX44_H
00019 # include <BALL/MATHS/matrix44.h>
00020 #endif
00021 
00022 #ifndef BALL_KERNEL_FRAGMENT_H
00023 # include <BALL/KERNEL/fragment.h>
00024 #endif
00025 
00026 namespace BALL 
00027 {
00028   class FragmentDB;
00029 
00033   class BALL_EXPORT ReconstructFragmentProcessor 
00034     : public UnaryProcessor<Fragment> 
00035   { 
00036     
00037     public:
00038 
00042 
00048     ReconstructFragmentProcessor();
00049 
00054     ReconstructFragmentProcessor(const FragmentDB& db);
00055 
00058     ReconstructFragmentProcessor(const ReconstructFragmentProcessor& db);
00059 
00062     virtual ~ReconstructFragmentProcessor();
00063 
00065 
00068 
00071     virtual bool start();
00072     
00075     virtual bool finish();
00076     
00081     virtual Processor::Result operator() (Fragment&);
00082 
00084 
00088     
00091     list<Atom*>& getInsertedAtoms();
00092 
00095     Size getNumberOfInsertedAtoms() const;
00096 
00099     void setFragmentDB(const FragmentDB& fragment_db);
00100 
00103     const FragmentDB* getFragmentDB() const;
00104 
00106 
00110     // ???? This should be replaced by the corresponding method in StructureMapper
00111     // We don't need two implementations with the same code.
00124     static Matrix4x4 mapThreeVectors
00125       (const Vector3& w1, const Vector3& w2, const Vector3& w3,
00126        const Vector3& v1, const Vector3& v2, const Vector3& v3);
00127 
00134     static Triple<bool, const Atom*, const Atom*>
00135     getTwoReferenceAtoms(const Atom& ref_center_atom, const HashSet<const Atom*>& allowed)
00136       ;
00137 
00140     static list<Atom*> reconstructFragment(Fragment& frag, const Fragment& tplate);
00142 
00143     protected:
00144     
00145     /*_ @name Protected attributes
00146     */
00147     //_@{
00148 
00149     /*_ Pointer to the fragment DB 
00150     */  
00151     const FragmentDB* fragment_db_;
00152     
00153     /*_ List of atoms inserted during the last application of the processor.
00154     */
00155     list<Atom*> inserted_atoms_;
00156     //_@}
00157   };
00158   
00159 } // namespace BALL
00160 
00161 #endif // BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H